Intro: Donatello narrates as we view a Triceraton Tribase half-submerged in the bay. Panning around the scene, we see various alien wreckage. Zooming in, we see three giant Amazonian Blade Bots coming right for the Turtles!
Act 1: Open at Oroku Saki’s midtown mansion as a press conference is in progress. Saki stands at a podium discussing his work to "help" the city and then begins addressing questions. As one reporter asks Saki about his ties to the criminal organization known as the Foot Clan and his association to the street gang called the Purple Dragons, Karai moves in and elbows the investigator in the side, knocking him to his knees. Karai waves off the onlookers and escorts the man out.
Cut to the Turtles running on some rooftops overlooking Central Park. The guys are practicing and decide to play "hide 'n' seek" - Don is "it". The brainy Turtle quickly finds his brothers, but he was cheating by using his night-vision goggles. Just as Raph and Mike are about to pummel their bro for not playing fair, Don's Shell Cel rings. Donatello answers his phone, but his ears are blasted by the grating screech of a Fax - a curiosity that's been occurring more often lately. Suddenly, a group of Foot helicopters, escorted by some police whirlybirds, fly in and haul off parts of Triceraton technology. The Turtles are surprised that New York's Finest are assisting Saki's minions and decide to investigate.
Our heroes enter Central Park to get a better look at the operation. While hidden in the shadows of the trees a safe distance away, the Turtles are suddenly assaulted by a group of Foot ninjas that erupt from woods. A battle ensues and the TMNT are surprised to discover that these Foot soldiers are more skilled than any they've met before.
Act 2: As they fight, the Turtles realize that these Foot are, indeed, much better trained than any regular Foot ninjas that they've faced before. Leonardo notes that their fighting style is oddly familiar. Just then, some police choppers approach and both the Foot and the TMNT disappear into the shadows.
Back at Saki’s mansion, the leader of the Foot Clan assures the mayor that he is not involved in any illegal activity as they both look over plans for refurbishing Times Square. The politician's misgivings are quickly forgotten when Saki offers to donate $100,000,000.00 more than the city asked for in reparation funds.
The Turtles have sought shelter underneath an old stone bridge. As they hide from the choppers, they realize that the Shredder has bought the salvaging rights to "clean up" New York City just so he can get his hands on all the alien technology left by the Triceraton invaders. The guys head back into the sewers to discuss plans on how they can stop Saki. Donatello determines their best bet is sabotage. Raph and Mikey are cheered by the thought that they'll get to “break stuff”.
At the mansion, Hun interrupts Saki's meeting with the mayor to report urgent news. The Shredder is enraged by his underling's appearances and orders him out of the room. The mayor notes Hun's Purple Dragon tattoo, but Saki explains that the dragon is a symbol of power in his culture. Considering Saki's donation, the mayor accepts this explanation and departs.
Saki boards an elevator and takes it down to his command center. The evil mastermind is greeted by Baxter Stockman, Hun and Karai. Hun attempts to apologize for interrupting the meeting. Saki grabs his wrist, twisting it painfully and forcing the giant to his knees. Shredder angrily informs Hun that he is not to be seen when legitimate business deals are being made.
A new scientist named Chaplin arrives and informs his boss that he has created a new group of robotic soldiers called the Amazonian Blade Bots. Three huge robots enter the room, each bearing Karai's likeness (Chaplin is obviously smitten with Karai, but she rebuffs his attempted tribute to her). Baxter is surprised that the newbie has been given the opportunity to head up his own division of Foot Tech and Saki sneers that if Chaplin's work is a success, perhaps Stockman can be removed - permanently. Hun laughs at his rival and then states that Karai should test the robots. Saki agrees and Karai battles her mechanoid dopplegangers, which defeat her in short order. Shredder orders the fight to be stopped just as Karai is about to be cleaved in two. The evil overlord and Karai prepare to leave to make plans, and Hun is surprised that he's not involved in the scheming. This gives Baxter the opportunity to mock the big man.
Act 3: The Turtles have swum into the bay and are investigating the fallen Tribase. Our heroes infiltrate the crashed spacecraft, which is half submerged in the water. As they enter, the TMNT find a cargo bay full of explosives. Our heroes continue their journey to the center of the ship and spy a group of Foot Tech operatives salvaging the gigantic power core from the craft. Deciding that the scientists will be no match for their skills, the Turtles attack. Once again the Gang Green is surprised by the fighting prowess of their foes, who take the upper hand in the battle. Leo realizes that their familiar fighting style is that of Karai’s, which means that she must still be working for Shredder. Focusing their efforts, the TMNT defeat the salvage crew and investigate the power core. Donatello wants to find a way to destroy the device without causing tremendous collateral damage when a drop of water illustrates how this can be achieved - they can short-circuit the power core by flooding it with liquid. The Turtles decide they’ll use the explosives to sink the Tribase completely, thus filling it with water which should deactivate the core. The TMNT head back to the cargo bay and grab a bunch of explosives and a detonator with a timer. Don sets the timer for ten minutes - which should give them more than enough time to escape - but as the Turtles begin to make their way out of the vessel, they're met by the three Amazonian Blade Bots.
Act 4: As they battle, the first round of bombs go off and the Tribase is flooded and begins to sink. The Turtles and the Bots are washed away in the torrent of water.
In the control room, Chaplin is distressed that his creations are in trouble. However, the pilots of the mechanoids have things in control and the Bots escape harm - giving the new Foot Tech scientist cause to celebrate. Baxter Stockman watches with distain and decides that he'll have to sabotage the Bots, lest he lose his status with the Foot Clan.
The Turtles make their way to their escape route, but are confronted by the golden Blade Bot. The TMNT's weapons are of little use, but they disarm the robot and Leo uses its spear to cut it in half. The guys once again try to take their leave, but the other two Blade Bots arrive.
The TMNT prepare for another battle when Baxter's treachery takes effect - the Amazonian Blade Bots short-circuit and fall into the cargo bay full of explosives. Don yells at his brothers to run and the TMNT scramble to get away, just as the sparks from the malfunctioning robots ignite the explosives. The Turtles make it out of the Tribase just as it explodes into a ball of flame and sinks into the water. As our heroes watch smoke billow into the sky, they hear an approaching craft. The Turtles turn to see Karai arrive in a speed boat. Saki calls her on the radio to see if the TMNT have been destroyed - there's a tense moment as the Turtles stare at their former ally. Karai reports to her master that the Turtles have escaped and then she zooms off in the boat. Mikey complains that she could have given them a ride and Raph smacks his jovial brother on the head.
Cut the command center, where Shredder is admonishing his underlings for their failures. Unexpectedly, Saki states that the entire Tribase mission was merely a distraction planned by Karai to distract the Turtles while the true goal was accomplished. With that we see a container being loaded into the elevator with Shredder and Karai. Stockman and Hun try to ingratiate themselves into this new mission, but the elevator doors close.
Inside, Karai asks her master about the salvage mission, as its costs are dangerously high. Saki merely smiles and pats the container, stating that where he's going, money is meaningless.